The NSK arduino boards were not working on ubuntu as expected.The fix for this is quite simple,

Connect the reset pin to 3.3V or 5V and then program the arduino. It should work. Im still not sure if this was an error with the FTDI hardware, or if its the software causeing the issue. Im guessing its the ftdi driver on linux which is negating the DTR line. If someone can fix that it would be great.

But as of now, those of you who had the NSK boards can now use it on ubuntu with no issue. Just connect the 5V or 3.3V to the reset pin.